TB-Profiler result

Run: SRR13861737
Summary

Run ID: SRR13861737

Sample name:

Date: 2024-04-16T03:25:20.258777

Number of reads: 433357

Percentage reads mapped: 7.23

Median coverage: 13.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4 Euro-American None 1.0
lineage4.9 Euro-American (H37Rv-like) None 1.0
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid
ethambutol embR p.Ser188Arg Mutation from literature
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid
delamanid
bedaquiline
linezolid
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence Comment
embR 1416784 p.Ser188Arg missense_variant 1.0 ethambutol Mutation from literature
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence
fgd1 490771 c.-12T>G upstream_gene_variant 1.0 clofazimine
pretomanid
delamanid
mshA 575112 c.-236G>T upstream_gene_variant 1.0 ethionamide
isoniazid
rpoB 761125 c.1320dupG frameshift_variant 1.0 rifampicin
rpoB 761989 p.Ala728Val missense_variant 1.0 rifampicin
rpoC 763884 p.Ala172Asp missense_variant 1.0 rifampicin
rpoC 765936 p.Ala856Gly missense_variant 1.0 rifampicin
mmpL5 776303 c.2178G>C synonymous_variant 1.0 clofazimine
bedaquiline
rplC 800132 c.-677C>G upstream_gene_variant 1.0 linezolid
fbiC 1303334 p.Gly135Val missense_variant 1.0 clofazimine
pretomanid
delamanid
embR 1416250 c.1098C>A synonymous_variant 1.0 ethambutol
rrs 1472936 n.1091C>T non_coding_transcript_exon_variant 0.52 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.5 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.5 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.5 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 0.5 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472963 n.1118G>A non_coding_transcript_exon_variant 0.52 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472971 n.1126G>C non_coding_transcript_exon_variant 0.54 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472973 n.1128_1130delAATinsCG non_coding_transcript_exon_variant 0.56 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.54 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.54 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.54 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.56 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.56 streptomycin Uncertain significance
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1473002 n.1157G>T non_coding_transcript_exon_variant 0.58 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.54 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.54 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.54 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473044 n.1199C>G non_coding_transcript_exon_variant 0.5 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473051 n.1206T>C non_coding_transcript_exon_variant 0.41 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473053 n.1208T>G non_coding_transcript_exon_variant 0.41 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1474218 n.561T>C non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.72 capreomycin
linezolid
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.8 capreomycin
linezolid
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.8 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.8 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.82 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.85 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.85 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.85 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.84 capreomycin
linezolid
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.84 capreomycin
linezolid
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.84 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.84 capreomycin
linezolid
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.86 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.86 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.86 capreomycin
linezolid
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.86 capreomycin
linezolid
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.85 capreomycin
linezolid
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.85 capreomycin
linezolid
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.84 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.84 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.54 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid
rpsA 1833707 p.Gly56Arg missense_variant 1.0 pyrazinamide
tlyA 1918168 p.Phe77Leu missense_variant 1.0 capreomycin
bacA 2063041 p.Arg563Pro missense_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
bacA 2063427 c.1302G>T synonymous_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
bacA 2063999 c.729_730insT frameshift_variant 1.0 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
ndh 2103307 c.-265A>G upstream_gene_variant 1.0 ethionamide
delamanid
isoniazid
kasA 2518023 c.-92C>T upstream_gene_variant 1.0 isoniazid
folC 2747689 c.-91C>T upstream_gene_variant 1.0 para-aminosalicylic_acid
whiB7 3569132 c.-453C>T upstream_gene_variant 1.0 streptomycin
amikacin
kanamycin
Rv3236c 3613708 c.-592C>G upstream_gene_variant 1.0 pyrazinamide
clpC1 4038389 c.2316G>C synonymous_variant 1.0 pyrazinamide
clpC1 4040326 p.Leu127Val missense_variant 1.0 pyrazinamide
glpK 4139633 c.123C>A synonymous_variant 1.0 ethambutol Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
embC 4241920 p.Asp686Glu missense_variant 1.0 ethambutol
ubiA 4269209 p.Ser209Thr missense_variant 1.0 ethambutol